1 Answer
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Yes, setup one FTP site and link each of these directories as Virtual Directories from within the IIS FTP manager. For security make sure the permissions separate these out from accessibility by using the R/W allow and deny rights.

I tried this, however when I connect to the FTP site I just see the empty directory, none of the virtual directories I have set up. I only have anonymous access setup with pass through authentication....am I doing something wrong?
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user47587Oct 27 '10 at 21:53

try changing to one of the directories, this might be the NTFS permissions on that directory unable to display. see if you can run the command 'cd directoryname' and if it accepts in order to run a process of elimination.
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Nick O'NeilOct 27 '10 at 22:55

OK, I get the error "Error details: File system denied the access.". I get that error when trying to cd to the directory, but in the root directory it does not show up with ls. How should I grant permissions?
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user47587Oct 27 '10 at 23:25

One of the directories not having permission is weird, because previously I just added it as the main site and it worked fine
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user47587Oct 28 '10 at 0:14

from explorer, right click the directory check the ntfs permissions, be sure that the logged in user has the appropriate permissions to allow read and director listing if required.
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Nick O'NeilOct 28 '10 at 1:26